Module 1 Flashcards

Question

12. Antiphospholipid antibody syndrome (APLAS), a disorder strongly associated with recurrent miscarriages, frequently manifests as having detectable antibodies in the blood directed against * phosphatidylinositol. * phosphatidylserine. * phosphatidylcholine. * phosphatidylethanolamine. * diphosphatidylglycerol.

Answer 1

**e. Diphosphatidylglycerol** Antibodies against diphosphatidylglycerol (cardiolipin) often develop in antiphospholipid antibody syndrome (APLAS). Reference: 2023 Biochem Ratio

Answer 2

**c. A hydrocarbon chain attached to sn-1 of glycerol via an ether bond** The fatty acid at the sn-1 carbon of a glycerophospholipid is replaced by an unsaturated alkyl group attached by an ether (rather than an ester) linkage to the core glycerol molecule References: Rodwell, V. W., Bender, D. A., Botham, K. M., Kennelly, P. J., & Weil, P. A. (2018). Harpers illustrated biochemistry. New York: McGraw-Hill Medical. Ferrier, D. R. (2017). Lippincott illustrated reviews: Biochemistry. Philadelphia: Wolters Kluwer.

Answer 3

**b. Glycerophospholipid** A glycerophospholipid consists of a glycerol backbone and an ester. In the structure, the one encircled is a glycerol backbone connecting the 2 esters and phosphatidylcholine. In DPPC, positions 1 and 2 on the glycerol are occupied by palmitate. Reference: Ferrier, D. R. (2017). Lippincott illustrated reviews: Biochemistry. Philadelphia: Wolters Kluwer.

Answer 4

**d. They differ in the configuration around one carbon atom only** Isomers that differ in configuration of the -OH and -H on carbon atoms 2, 3, and 4 of glucose are defined as epimers of each other.

Answer 5

**b. Ubiquitin** Lysosomal protease, a major pathway for protein degradation, does not use ATP but involves ubiquitin. Ubiquitin is a small, highly conserved protein that tags various proteins for degradation in proteasomes. The ubiquitin pathway is associated with the disposal of misfolded proteins and regulatory enzymes that have short half-lives. Polyubiquitinated target proteins enter proteasomes in the cytosol, which is composed of 4 rings with the protease active sites and 1 or 2 caps that recognize the polyubiquitinated substrates and initiate degradation. Target proteins unfold via ATPase in the cap. Target proteins are degraded to small peptides in the core and further degraded by cytosolic peptidases once out of the proteasome. Reference: Harper’s Illustrated Biochemistry 31st edition. Chapt. 49

Answer 6

b. Nuclear exportation

Answer 7

b. ER importation

Answer 8

**a. Nuclear importation** In nuclear import, proteins to be imported carry a nuclear localization signal (NLS). One example of an NLS is the amino acid sequence (Pro)2(Lys)3-Arg-Lys-Val, which is markedly rich in basic residues.

Answer 9

**d. ER to Golgi Complex to Vesicles to Plasma Membrane** Proteins synthesized and sorted in the RER branch include many destined for various membranes (eg, of the ER, Golgi apparatus [GA], plasma membrane [PM]) as well as lysosomal enzymes, and also those for export from the cell via exocytosis (secretion).These various proteins may thus reside in the membranes or lumen of the ER, or follow the major transport route of intracellular proteins to the GA. In the secretory or exocytotic pathway, proteins are transported from the ER → GA→ PM and then released into the external environment. Reference: Harper’s Illustrated Biochemistry 30th ed. Chap 49 pg. 608

Answer 10

**a. Peroxisomal importation** Reference: Doc Raymond ppt

Answer 11

**a. Mitochondrial importation** Reference: Doc Raymond ppt

Answer 12

**d. COPII** A number of proteins possess the amino acid sequence KDEL (Lys-Asp-Glu-Leu) at their carboxyl terminal KDEL-containing proteins first travel to the GA in vesicles coated with coat protein II (COPII). This process is known as anterograde vesicular transport. In the GA they interact with a specific KDEL receptor protein, which retains them transiently. They then return to the ER in vesicles coated with COPI (retrograde vesicular transport), where they dissociate from the receptor, and are thus retrieved. HDEL sequences (H = histidine) serve a similar purpose. Reference: Harper’s Illustrated Biochemistry 30th ed. Chap 49 pg. 621

Answer 13

**b. The outer membrane leaflet** Sphingomyelin are found in the outer leaflet of the cell membrane and are particularly abundant in specialized areas of the plasma membrane known as lipid rafts. Reference: Harper’s Illustrated Biochemistry 31st ed. Chap 21 pg. 200

Answer 14

**b. Cholesterol-enriched membrane invaginations** Lipid rafts are specialized areas of the outer leaflet of the lipid bilayer enriched in cholesterol, sphingolipids, and certain proteins. Caveolae may derive from said lipid rafts. Reference: Harper’s Illustrated Biochemistry 31st ed. Chap 40 pg. 466

Answer 15

**c. Integral membrane protein** Most membrane proteins fall in the integral class, meaning that they interact extensively with the phospholipids and require the use of detergents for their solubilization. Reference: Harper’s Illustrated Biochemistry 31st ed. Chap 40 pg. 464-465

Answer 16

**d. Proteasome in the cytoplasm** Improperly folded ER proteins are exported and degraded in the cytosol. Dr. Raymond Cruz’ ppt. Slide 51

Answer 17

**a. Proteins are the most abundant type of macromolecules within cell membranes** The basic structure of all membranes is the lipid bilayer. This bilayer is formed by two sheets of phospholipids in which the hydrophilic polar head groups are directed away from each other and are exposed to the aqueous environment on the outer and inner surfaces of the membrane. Reference: Harper’s Illustrated Biochemistry 30th ed. Chap 40 pg. 497

Answer 18

**d. They bind to the same substrate but produce different products** Lactate dehydrogenase is comprised of two domains, an N-terminal NAD+-binding domain and a C-terminal binding domain for the second substrate, pyruvate. Reference: Harper’s Illustrated Biochemistry 30th ed. Chap 5 pg. 40

Answer 19

**b. Enzyme Y, Km = 2.25** A numerically small (low) Km reflects a high affinity of the enzyme for substrate, because a low concentration of sub strate is needed to half saturate the enzyme—that is, to reach a velocity that is ½ Vmax. Reference: Lippincott's Illustrated Reviews Biochemistry 6th ed. Chap 5 pg. 59

Answer 20

**e. Covalent catalysis** The process of covalent catalysis involves the formation of a covalent bond between the enzyme and one or more substrates. Covalent catalysis is particularly common among enzymes that catalyze group transfer reactions. Residues on the enzyme that participate in covalent catalysis generally are cysteine or serine, and occasionally histidine Reference: Harper’s Illustrated Biochemistry 30th ed. Chap 7 pg. 63

Answer 21

**c. Simple feed-back inhibition** Types of Feed-back inhibition : 1. Simple feed-back inhibition. The final product (E) inhibits the step from A to B. 2. Co-operative feed-back inhibition. Both final products (D, E) inhibit the first step of their own synthesis together. 3. Multivalent feed-back inhibition. 4. Inhibition at a ramification of a biosynthesis pathway (sequential inhibition)

Answer 22

**b. Cyclooxygenase** Prostanoid synthesis involves the consumption of two molecules of O2 catalyzed by cyclooxygenase (COX) (also called prostaglandin H synthase), an enzyme that has two activities, a cyclooxygenase and peroxidase. COX is present as two isoenzymes, COX-1 and COX-2. The product, an endoperoxide (PGH), is converted to prostaglandins D and E as well as to a thromboxane (TXA2) and prostacyclin (PGI2). Each cell type produces only one type of prostanoid. The NSAID aspirin inhibits COX-1 and COX-2. Other NSAIDs include indomethacin and ibuprofen, and usually inhibit cyclooxygenases by competing with arachidonate. Since inhibition of COX-1 causes the stomach irritation often associated with taking NSAIDs, attempts have been made to develop drugs which selectively inhibit COX-2 (coxibs).

Answer 23

**c. Competitive** Competitive - inhibitor has no effect on Vmax but raises K′m

Answer 24

**a. There is an associated formation of weak attractive bonds between the enzyme and substrate** Enzymes lower the activation energy by utilizing the free energy called binding energy. Binding energy is the free energy released by the formation of a large number of weak interactions between a complementary enzyme and substrate. Reference: Biochemistry: A Short Course 3rd ed. Chap 6.4 pg. 105 Emil Fischer proposed that enzymes and their substrates interact to form an enzyme-substrate (ES) complex Reference: Harper’s Illustrated Biochemistry 30th ed. Chap 7 pg. 62

Answer 25

**b.It usually uses small molecules such as CH3 for activation and inactivation** COVALENT MODIFICATION * The covalent attachment of another molecule can modify the activity of enzymes and many other proteins * In these instances, a donor molecule provides a functional moiety that modifies the properties of the enzyme * Most modifications are reversible, unlike proteolytic reactions * Phosphorylation and dephosphorylation are the most common methods of covalent modification (sulfation, acetylation, methylation are less common)

Answer 26

**b. General acid/base catalysis**

Answer 27

**b. Isomerase** Isomerase, a class of enzymes that catalyze reactions involving a structural rearrangement of a molecule. This step in glycolysis is catalyzed by triose phosphate isomerase. Isomerases catalyze isomerization reactions (geometric/structural changes). This step completes the first phase of glycolysis. Reference: Cruz, R. (n.d.).Powerpoint presentation: Enzymes.

Answer 28

**b. Cellular response is faster with allosteric control than by controlling enzyme concentration in the cell** *ALLOSTERIC ENZYMES* * Bind small, physiologically important molecules to modulate enzymes * Usually contain multiple subunits and frequently catalyze the committed step early in a pathway * The small regulatory molecules to which they bind are known as effectors * The hallmark of effectors is that when they bind to enzymes, they alter the catalytic properties of an enzyme’s active site * Those that increase catalytic activity are known as positive effectors (ACTIVATORS) * Effectors that reduce or inhibit catalytic activity are negative effectors Allosteric modulators do not bind to the active site. Allosteric regulation is dependent on the binding of allosteric activator/inhibitor on the enzyme which causes a conformational change of the active site. Allosteric regulators usually regulate the first step in the reaction pathway and not the last step.

Answer 29

**b. Proximity and orientation effect** “Proximity: Reaction between bound molecules doesn’t require an improbable collision of 2 molecules. They’re already in “contact” (increases local concentration of reactants).” “Orientation: Reactants are not only near each other on enzyme, they're oriented in optimal position to react. The improbability of colliding in correct orientation is taken care of.” Reference: Cruz, R. (n.d.).Powerpoint presentation: Enzymes.

Answer 30

**a. the activation energy needed to bring the reactants to the transition state** “When the activation energy is lower, more molecules have the energy required to reach the transition state and more product will be formed faster… _The essence of catalysis is stabilization of the transition state_.”

Answer 31

**d. Transaminase** Aminotransferases, also called transaminases, serve a diagnostic function. “The presence of alanine and aspartate aminotransferase in the blood indicates liver damage. Liver damage can occur for a number of reasons, including viral hepatitis, long-term excessive alcohol consumption and reaction to drugs such as acetaminophen. Under these conditions, liver cell membranes are damaged and some cellular proteins, including the aminotransferases, leak into the blood.” Normal blood value for alanine and aspartate aminotransferase activity: 5-30 units/l and 40-125 units/l (value can reach 200-300 units/l depending on the extent of liver damage.

Answer 32

**c. Desolvation effect** “The close association between the active site and the substrate means that water is usually excluded from the active site unless it is a reactant. The nonpolar microenvironment of the cleft enhances the binding of substrates as well as catalysis.”

Answer 33

**b. Active site inhibition** Active site- recognition site for binding substrates; provides the environment wherein chemical transformation takes place. Competitive inhibitors- binds to the active site thereby blocking access by the substrate

Answer 34

**c. Strain effect** Enzymes that catalyze lytic reactions, chemical transformations that involve breaking a covalent bond, typically bind their substrates in a conformation that is somewhat unfavorable for the bond targeted for cleavage. This strained conformation mimics that of transition state intermediate. T_he resulting strain selectively distorts or stretches the targeted bond, weakening it and making it more vulnerable to cleavage_

Answer 35

**b. 2, 1, 4, 3** Action potential produces depolarization then the excitatory transmitter opens Ca2+ channels causing the neurotransmitter release Reference:Ganong’s Review of Medical Physiology 26th ed. Chap 6 pg. 124-126

Answer 36

**d. Vitamin C is an essential cofactor in the hydroxylation process** Hydroxyproline is formed by the posttranslational hydroxylation of peptide-bound proline residues catalyzed by the enzyme prolyl hydroxylase, whose cofactors are ascorbic acid (vitamin C) and α-ketoglutarate. Reference: Harper’s Illustrated Biochemistry 31st Ed. page 593 / Dr. Cruz ppt

Answer 37

**a. Lysyl Oxidase: Cuprous Ion** - Transaminase enzymes require pyridoxal phosphate - Prolyl hydroxylase requires Ascorbic Acid (Vitamin C), NOT pyridoxal phosphate - Lysyl Hydroxylase requires Ascorbic Acid (Vitamin C) and Cuprous Ion

Answer 38

d. Hyperammonemia Abnormalities in Collagen Synthesis: * Ehlers-Danlos syndrome - hyperextensibilty of skin, abnormal tissue fragility, increased joint mobility * Alport syndrome - Presenting sign is hematuria and patient may develop End-stage renal disease * Scurvy-Bleeding gums, subcutaneous hemorrhage, poor wound healing * Hyperammonemia is not an abnormality in collagen biosynthesis.

Answer 39

**b. Results from an insertion or deletion in a DNA sequence** Frameshift Mutation - insertions and deletions that do not involve three nucleotides or multiples of three nucleotides change the translation of all the mRNA downstream of the mutation

Answer 40

**d. It has intramolecular desmosine cross-links in its structure**

Answer 41

**b. Fibrillin** - Most cases of Marfan’s syndrome (an autosomal dominant disease), are caused by mutations on chromosome 15 for Fibrillin - Marfan’s syndrome patients have lens dislocation (ectopia lentis), long digits (arachnodactylyl) with hyperextensible joint, and weakness of the aortic media leading to dilation of ascending aorta Laminin- In muscular dystrophy, Laminin 2 is deficient; causing loss of function resulting in muscle weakness and atrophy Estrogen- Inhibits Osteoclasts formation Collagen: * Epidermolysis Bullosa → Collagen Type VII * Alport Syndrome → Collagen Type IV, found in basement membrane of renal glomeruli; Presenting sign: hematuria and may develop into end stage renal disease * Ehler’s Danlos → Collagen Type IV (most serious; spontaneous artery rupture on bowel, reflecting abnormal Collagen Type III); Type VI (due to deficiency in lysyl hydroxylase)

Answer 42

b. The inorganic component is mainly hydroxyapatite

Answer 43

**b. Glycine** The side chain of glycine, an H atom, is the only one that can fit into the crowded center of a three-stranded helix. Hydrogen bonds linking the peptide bond NH of a glycine residue with a peptide carbonyl (C═O) group in an adjacent polypeptide help hold the three chains together

Answer 44

**a. They are long, branched, homopolysaccharides attached to Amino Acids** Glycosaminoglycans * Most abundant heteropolysaccharide in the body * Has different functions * Made of * Complex amino sugars and uronic acids * Sulfate groups (except for Hyaluronic Acid) * Unbranched polysaccharides made of disaccharide units contain either of the two modified sugars-- N-acetylgalactosamine (GalNac) or N-acetylglucosamine (GlcNac) * Negatively charged * High viscosity to solution * Ideal for lubricating fluids, structural integrity to cells, and cell migration passageways

Answer 45

**c. Extracellularly** After processing and assembly of type I procollagen is completed, it is secreted into the extracellular space. During or following exocytosis, extracellular enzymes, the procollagen peptidases, remove the N-terminal and C-terminal propeptides.

Answer 46

**b. Accumulation of GAG in the cell** The mucopolysaccharidoses (MPSs) are a family of inherited disorders of GAG degradation. (Rodaks, p.481) They are due to lysosomal storage abnormalities, which allow the proliferation and non-degradation of GAG in cells. There is no synthesis abnormality involved because the problem is in degradation. No DNA mutation or Gogli complex defect is involved.

Answer 47

**b. False** The entire haploid genome contains sufficient DNA to code for nearly 1.5 million average-sized protein coding genes (i.e., ~2200 bp of protein- coding DNA). However, early studies of mutation rates and of the complexities of the genomes of higher organisms suggested that humans have significantly fewer than 100,000 proteins encoded by the ~1% of the human genome that is composed of exonic DNA. This implies that most genomic DNA is non protein coding—that is, its information is never translated into an amino acid sequence of a protein molecule.

Answer 48

**b. Inhibits the 50s ribosomal subunit**

Answer 49

b. False Each codon represents a particular amino acid, and each codon (20) is recognized by a specific tRNA

Answer 50

**a. Erythromycin** Erythromycin is an antibiotic that inhibits protein synthesis by inhibiting translocation during translation. It specifically acts on the 50s subunit of the ribosome. Tetracyclin inhibits aminoacyl tRNA binding on the A-site Streptomycin inhibits codon-anticodon initiation and elongation Lincomycin inhibits peptidyl transferase

Answer 51

**d. inactivation of the aminoacyl tRNA binding site** Tetracycline is a broad spectrum polyketide antibiotic produced by the Streptomyces genus of Actinobacteria. It exerts a bacteriostatic effect on bacteria by binding reversible to the bacterial 30S ribosomal subunit and blocking incoming aminoacyl tRNA from binding to the ribosome acceptor site.

Answer 52

**d. 3’ to 5’ exonuclease activity of DNA Pol delta** 5’ to 3’ Polymerase – ability to add nucleotides 3’ to 5’ Exonuclease – proofreading capacity 5’ to 3’ Exonuclease – removes primers

Answer 53

**c. CpG on the promoter site of the gene** FMR protein is needed for normal brain development. Full mutation causes the FMR1 gene to shut down or silence. Silencing of the FMR1 gene means no production of the FMR protein. Non production of the FMR protein is due to the methylation of the cytosine bases on the CGG repeat located on the CpG island proximal to the promoter region of the gene. The presence of numerous methyl groups on the CGG repeat will inhibit the formation of the transcriptional apparatus on the promoter site. Reference: Prof. Torres handout re Fragile X Syndrome

Answer 54

**b. 30** In DNA molecules, the concentration of deoxyadenosine (A) nucleotides equals that of Thymidine (T) nucleotides (A=T), while the concentration of deoxyguanosine (G) nucleotides equals that of deoxycytidine (C)nucleotides (G=C) Chargaff’s Rule (A+G=C+T) In this case, 20% Tymine=20% Adenine → 40% 100%-40%= 60% (C-G) 60%/2= 30% 30% Cytosine 30% Guanine Reference: 2023 Trans on Nucleic Acid (Dr. Sheila Torres)

Answer 55

**a. True** Termination occurs when the A site reaches a stop codon. There are no anticodon complementary to stop codon present in tRNA, the ribosome ”pauses” until it “falls off” the mRNA and the polypeptide chain terminates. This process is facilitated by a release factor protein that binds into the ribosomal A site containing a stop codon to help with protein release.

Answer 56

**a. 3’UTR** Messenger RNA * Composed of the 5’UTR, 3’UTR, and coding region * The 5’UTR is composed of: * Shine Dalgarno sequence (prokaryotic) * Kozac Consensus (eukaryotic) - G cap (eukaryotic) * 3 U’TR contains the poly A tail Reference: Prof. Shiela’s discussion on DNA and Protein synthesis

Answer 57

**d. Arginine, Glycine, Aspartic acid** Fibronectin contains an Arg-Gly-Asp (RGD) sequence that binds to the integrin receptor. This sequence is shared by a number of other proteins present in the ECM that bind to integrins present in cell plasma membranes, and its presence in synthetic peptides enables them to inhibit the binding of fibronectin to cells Reference: Harper’s Illustrated Biochemistry 31st Ed. page 597

Answer 58

**d. peptidyl transferase** The mode of action of chloramphenicol is in the ribosome specifically the prokaryotic peptidyl transferase. Chloramphenicol is an antibiotic. Chloramphenicol is effective against a wide variety of microorganisms, but due to serious side-effects (e.g., damage to the bone marrow, including aplastic anemia) in humans, it is usually reserved for the treatment of serious and life-threatening infections (e.g., typhoid fever). Chloramphenicol is bacteriostatic but may be bactericidal in high concentrations or when used against highly susceptible organisms.

Answer 59

**a. transversion** Single-base changes (point mutations) may be transitions or transversions. In the former, a given pyrimidine is changed to the other pyrimidine or a given purine is changed to the other purine. Transversions are changes from a purine to either of the two pyrimidines or the change of a pyrimidine into either of the two purines, as shown in Figure 37–3.

Answer 60

c. the lac transcription factors and the mammalian activators Regulatory elements Classified into two types, based on their “location” * Cis-acting elements - DNA sequences that exert their effect only on nearby genes Example: TATA box, enhancers and silencers ν * Trans-acting elements - Regulatory proteins that bind to such DNA sequences Example: Reference: Gene Expression Compendium by Sheila Maria P. Torres M.S.

Answer 61

**a. The electrochemical potential difference across the inner mitochondrial membrane caused by electron transport is positive on the matrix side.** The chemiosmotic theory, proposed by Peter Mitchell in 1961, postulates that the two processes are coupled by a proton gradient across the inner mitochondrial membrane so that the proton motive force caused by the electrochemical potential difference (negative on the matrix side) drives the mechanism of ATP synthesis. Reference: Rodwell, V. et. al. Harper’s Illustrated Biochemistry. (2018) Section III, Chapter 13, p. 121.

Answer 62

**a. binding of the glucagon by cell surface receptors initiates a chain of events that results in the phosphorylation of CREB protein**

Answer 63

b. oxidase. Oxidase removes hydrogen from a substrate and transfers it to oxygen to form water or hydrogen peroxide Reference: Page 4/8 of the handout on Biological Oxidation provided by Dr. Van Haute

Answer 64

**b. inducer** The allolactose serves as the inducer and binds to the receptor protein which in turn cannot bind to the O site due to conformational change in its structure Reference:. Doc Shiela’s Compendium on Gene Regulation and Mutation

Answer 65

**a. Initiator Element (Inr)** Trans-acting regulators are regulatory proteins that bind to such DNA sequences Ex: Transcription factors and other initiating factors (TBP) Cis-acting elements are DNA sequences that exert their effect only on nearby genes Ex: TATA box, enhancers, silencers Reference: Doc Shiela’s Compendium on Gene Expression

Answer 66

**c. –RT(ln Keq) is negative** Reference: Doc Van Haute’s Handout on Bioenergetics

Answer 67

c. Single Strand Binding Protein Explanation# 1: * Prokaryotic Enzymes of Replication The single-stranded DNA that result from the helicase action is coated with single-stranded DNA-binding protein that prevents reannealing of parental strands and prevent hairpins and other super secondary structures from forming in the sing stranded DNA Explanation# 2: * SSBs bind ssDNA with high affinity and in a sequence-independent manner and, in doing so, SSbs help to form central nucleoprotein complex substrates for DNA replication, recombination, and repair processes.

Answer 68

**c. Transversion, Missense** Purine- Adenine, Guanine (A & G) Pyrimidines- Cytosine, Thymine (C & T) _Point Mutation Types:_ 1. Transitions- interchanges of purines (A G) or pyrimidines (C T). 2. Transversions- interchanges of purine for pyrimidine bases or vice versa. * Ex. (A C), (A T), (G C), (G T) _Substitution Mutation Types:_ 1. Silent mutations have no effect on the protein. 2. Missense mutations result in a single amino acid change in the translated sequence. 3. Nonsense mutations result in an amino acid codon being replaced by a “stop” codon. Nonsense mutations end translation prematurely and result in a truncated protein.

Answer 69

**d. 2** Complex 4 transfers 2 hydrogen ions to the interstitial space. Since it is inhibited and then instead of 10 hydrogen ions only 8 hydrogen ions will be formed. Since 4 hydrogen ions are required for 1 ATP synthesis. Therefore 2 ATP will be produced Reference: handout in Oxidative phosphorylation provided by Dr. Van Haute

Answer 70

**d. Both NADH and FADH2 would not be rendered useless as electron carriers.** With rotenone intoxication, the ETC is expected to: * Coenzyme Q would still be able to transfer electrons, albeit via an alternate route. * ATP synthase, though left uninhibited, will be producing lesser amounts of ATP. * Only NADH is rendered useless, but FADH2 can still work as an electron carrier. **Except**: _Both NADH and FADH2 would not be rendered useless as electron carriers_ – Since Complex I is inhibited by Rotenone by inhibiting electron transfer of NADH from Complex I Fe-S center to CoQ, then NADH will be rendered useless but not FADH2 that conducts its electron transfer to Complex II. FADH is still capable to transfer its electron, but with less amount since ATP produced through Complex II (1.5 ATP) is less than ATP produced through Complex I (2.5 ATP) Reference: MODULE 1B. 15.) SAMPLE CONCEPT MAP: THE ROTENONE POISONING CASE

Answer 71

**b. Uncoupling of mitochondrial electron transport and oxidative phosphorylation**

Answer 72

**c. NAD+ and FAD** “NAD+ and FAD reacts directly with H+ to form NADH+ and FADH2 respectively.” Redox Reactions (Oxidation-reduction reactions) * Chemical reaction that involves a transfer of electrons between two chemical species (atom, molecule, or ion) * What is *Reduced* is the one accepting electrons. (the fuel in this example is carbohydrate)

Answer 73

**d. protein blocks the access of RNA Polymerase to the gene’s promoter region** Types of Gene Regulation: * Positive Regulation (Positive Transcriptional Control) – Expression of the genetic information is increased by the presence of specific regulatory element (activator/inducer) * Negative Regulation (Negative Transcriptional Control) – Expression of the genetic information is diminished by specific regulatory element (repressor). The repressor binds to the Operator to block the RNA polymerase from “going” to the structural gene in order to prevent it from transcribing unnecessary/unneeded protein. Reference: Doc Shiela’s Compendium on “Gene Regulation and Mutation”

Answer 74

**b.The ΔE is negative, while the ΔS is positive**

Answer 75

**b.nonsense mutation** Nonsense mutation - result in an amino acid codon being replaced by a STOP CODON. It ends translation prematurely and result in a truncated protein. Silent mutation - replacement of a single nucleotide with another, but have no effect on the protein (new codon can code for the same amino acid) Missense mutation - replacement of a single nucleotide with another, and results in a single amino acid change in the translated region

Answer 76

**c.all of the choices** This type of point mutation has a change in a single nucleotide of the organism’s DNA which affects RBC shape. Hence, there is a *change in O2 carrying capacity of Hgb.* The classic example is Sickle Cell Disease (SCD), caused by mutation of a single base, a T-A DNA Substitution, which in turns result to A-U change in mRNA corresponding to 6th codon of beta globin gene. The altered codon specifies a different amino acid, Valine rather than Glutamic Acid causing structural abnormality of the beta globin molecule leading to hemoglobin aggregation and RBC SICKLING.

Answer 77

**c.Succinate** Complex II is also known as Succinate Coenzyme Q Reductase. From the name itself, Succinate dehydrogenase (SDH; succinate: ubiquinone oxidoreductase; mitochondrial complex II) plays a central role in mitochondrial metabolism, catalyzing the oxidation of succinate to fumarate and the reduction of ubiquinone (UQ) to ubiquinol (UQH2). Source: Harpers Illustrated Biochemistry (31st Edition); Rodwell et.al; page 120.

Answer 78

**c. There are roughly 25 moles of product for every 100 moles of substrate**. Keq = [product]/[substrate] 25 mole of product divided by 100 moles of substrate, the resulting Keq is 0.25. Thus, “there are roughly 25 moles of product for every 100 moles of substrate.” Is the correct answer. Reference: 2023 ratio

Answer 79

**b. co-repressor** Tryptophan Operon * genes for the enzymes of tryptophan biosynthetic pathway * repressible genes=Genes whose expression is turned off by the presence of a repressor * The regulatory gene produces repressor but is inactive (apo-repressor) * The 5 structural genes produce proteins essential for tryptophan synthesis * In the absence of tryptophan, the operon is on * Inactive repressor cannot bind the operator site * Excess tryptophan represses transcription * Tryptophan acts as co-repressor that activates the apo-repressor * Binding of the activated repressor blocks RNA Pol transcription of the structural genes source:

Answer 80

**b. repressor** Binding of the repressor to the operator region does not allow the polymerase to bind to the promoter, hence stops gene expression.

Answer 81

**d. A reaction with +ΔG0' proceeds in a forward direction if the substrate concentration is raised high enough, and its product is rapidly cleared by a subsequent reaction.** Recall that metabolic pathways must have an overall negative △ G°(provided by ATP hydrolysis) to favor the formation of products over the formation of reactants. In that same vein, it is possible for reactions in the pathway with positive △ G°’ to proceed in the forward direction if: * The concentration of that reaction’s substrate is raised to a high enough level. This increase in substrate concentration is provided by the reaction preceding the + △ G°’ reaction in question along the metabolic pathway. * The concentration of that reaction’s product is decreased to a very low level. This occurs when the subsequent reaction (which uses the + △ G°’ reaction’s product as substrate) clears the product. These 2 processes cause disequilibrium as far as the + △ G°’ reaction is concerned because of more substrate and less product than usual compared to the levels present at equilibrium. In order to obtain equilibrium again, the + △ G°reaction has to move forward. This reiterates the fact that the direction if a reaction is dependent on the initial substrate and product concentration as reflected in Keq. While the general principle is “larger and more negative G°-\> spontaneous remains true, △ G°, however is not an indicator of the velocity of the reaction or the rate at which equilibrium can be reached. This actually depends on the efficiency and amount of enzyme available to catalyze the reaction.

Answer 82

**d. It has a high positive redox potential, thus easily oxidizes other molecules** Redox Potential (E0’) * A measure (in volts) of the energy change when that compound accepts e– * Expression of the willingness of a compound to accept electrons. * The more positive the Redox Potential, the more willing it is to accept electrons. * (More positive = Better as Oxidizing agent) That’s why it can easily oxidize other molecules. In contrast: * The more negative the Redox Potential, the more willing it is to give off electrons. * (More negative = Better as Reducing agent)

Module 1 Flashcards

1A - Amino Acids - Carbohydrates and Lipids - Membrane Receptor & Transport; Material Transport - Enzymes 1B ECM, DNA & Protein Synthesis, Gene Expression and Mutations, Bioenergetics, Biological Oxidation & Oxidative Phosphorylation (106 cards)